From e83e6d1a1c0b7016d864eca38047cd7f520c8d6a Mon Sep 17 00:00:00 2001
From: pbardou <philippe.bardou@inra.fr>
Date: Wed, 15 May 2019 15:18:12 +0200
Subject: [PATCH] IMAGE_calling :remove not allowed multithreading in GATK
command line
---
Snakemake/IMAGE_calling/Snakefile | 6 +++---
.../IMAGE_calling/resources_SLURM_memGlobal.yaml | 3 ---
.../IMAGE_calling/rules/combine_genotypeGVCF.rules | 14 ++++++--------
Snakemake/IMAGE_calling/rules/realignment.rules | 8 ++------
4 files changed, 11 insertions(+), 20 deletions(-)
diff --git a/Snakemake/IMAGE_calling/Snakefile b/Snakemake/IMAGE_calling/Snakefile
index 34abbf6..aa19053 100755
--- a/Snakemake/IMAGE_calling/Snakefile
+++ b/Snakemake/IMAGE_calling/Snakefile
@@ -39,8 +39,8 @@ rule_resources = {
"bwa_mem" : ["cpu"],
"sample_merge" : ["mem"],
"markduplicates" : ["mem"],
- "RealignerTargetCreator" : ["mem", "cpu"],
- "IndelRealigner" : ["mem", "cpu"],
+ "RealignerTargetCreator" : ["mem"],
+ "IndelRealigner" : ["mem"],
"qualimap" : ["mem", "cpu"],
"BaseRecalibrator_1" : ["mem" , "cpu"],
"PrintReads" : ["mem" , "cpu"],
@@ -48,7 +48,7 @@ rule_resources = {
"AnalyzeCovariates" : ["mem"],
"HaplotypeCaller" : ["mem","cpu"],
"CombineGVCFs" : ["mem"],
- "GenotypeGVCFs" : ["mem", "cpu"],
+ "GenotypeGVCFs" : ["mem"],
"bcftools_stats_gatk": ["cpu"],
"bcftools_stats_freebayes": ["cpu"],
"bcftools_stats_mpileup": ["cpu"]
diff --git a/Snakemake/IMAGE_calling/resources_SLURM_memGlobal.yaml b/Snakemake/IMAGE_calling/resources_SLURM_memGlobal.yaml
index d5fb390..06cc295 100644
--- a/Snakemake/IMAGE_calling/resources_SLURM_memGlobal.yaml
+++ b/Snakemake/IMAGE_calling/resources_SLURM_memGlobal.yaml
@@ -19,11 +19,9 @@ markduplicates:
RealignerTargetCreator:
mem: "30G"
- cpu : 8
IndelRealigner:
mem: "30G"
- cpu : 8
BaseRecalibrator_1:
mem: "50G"
@@ -55,7 +53,6 @@ CombineGVCFs :
GenotypeGVCFs :
mem : "60G"
- cpu : 8
partition : "unlimitq"
freebayes:
diff --git a/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules b/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
index 128b1a3..5432602 100644
--- a/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
+++ b/Snakemake/IMAGE_calling/rules/combine_genotypeGVCF.rules
@@ -61,7 +61,7 @@ def get_cohor_gvcf(wildcards):
rule GenotypeGVCFs:
input:
- gvcf=get_cohor_gvcf,
+ gvcfs=get_cohor_gvcf,
ref=config["reference_genome"]
output:
@@ -70,13 +70,11 @@ rule GenotypeGVCFs:
log:
"results/gatk_haplotypecaller/logs/GenotypeGVCFs.log"
- threads: config["GenotypeGVCFs"]["cpu"]
-
params:
mem=config["GenotypeGVCFs"]["mem"]
- shell:
- """
- java -Xmx{params.mem} -jar {config[bin][gatk]} -T GenotypeGVCFs -nct {threads} -R {input.ref} --variant {input.gvcf} -o {output} 2> {log}
- {config[bin][tabix]} -f -p vcf {output}
- """
+
+ run:
+ gvcfs=" --variant ".join(input.gvcfs)
+ shell("java -Xmx{params.mem} -jar {config[bin][gatk]} -T GenotypeGVCFs -R {input.ref} --variant {gvcfs} -o {output} 2> {log}")
+
diff --git a/Snakemake/IMAGE_calling/rules/realignment.rules b/Snakemake/IMAGE_calling/rules/realignment.rules
index 7d6493d..e2bb3d1 100644
--- a/Snakemake/IMAGE_calling/rules/realignment.rules
+++ b/Snakemake/IMAGE_calling/rules/realignment.rules
@@ -16,8 +16,6 @@ rule RealignerTargetCreator:
output:
temp("results/gatk_realignment/{sample}.rg.sort.md.intervals")
- threads: config["RealignerTargetCreator"]["cpu"]
-
log:
stderr="results/gatk_realignment/logs/{sample}_RealignerTargetCreator.stderr",
stdout="results/gatk_realignment/logs/{sample}_RealignerTargetCreator.stdout"
@@ -26,7 +24,7 @@ rule RealignerTargetCreator:
mem= config["RealignerTargetCreator"]["mem"]
shell:
- "java -Xmx{params.mem} -jar {config[bin][gatk]} -T RealignerTargetCreator --allow_potentially_misencoded_quality_scores -nct {threads} -R {input.ref} -I {input.bam} -o {output} 2> {log.stderr} > {log.stdout}"
+ "java -Xmx{params.mem} -jar {config[bin][gatk]} -T RealignerTargetCreator --allow_potentially_misencoded_quality_scores -R {input.ref} -I {input.bam} -o {output} 2> {log.stderr} > {log.stdout}"
rule IndelRealigner:
input:
@@ -38,8 +36,6 @@ rule IndelRealigner:
output:
temp("results/gatk_realignment/{sample}.rg.sort.md.real.bai"),
bam=temp("results/gatk_realignment/{sample}.rg.sort.md.real.bam")
-
- threads: config["IndelRealigner"]["cpu"]
log:
stderr="results/gatk_realignment/logs/{sample}_IndelRealigner.stderr",
@@ -49,4 +45,4 @@ rule IndelRealigner:
mem= config["IndelRealigner"]["mem"]
shell:
- "java -Xmx{params.mem} -jar {config[bin][gatk]} -T IndelRealigner --allow_potentially_misencoded_quality_scores -nct {threads} -R {input.ref} -I {input.bam} -targetIntervals {input.intervals} -o {output.bam} 2> {log.stderr} > {log.stdout}"
+ "java -Xmx{params.mem} -jar {config[bin][gatk]} -T IndelRealigner --allow_potentially_misencoded_quality_scores -R {input.ref} -I {input.bam} -targetIntervals {input.intervals} -o {output.bam} 2> {log.stderr} > {log.stdout}"
--
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